[2023-06-27 00:33:09,786] [INFO] DFAST_QC pipeline started.
[2023-06-27 00:33:09,875] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 00:33:09,875] [INFO] DQC Reference Directory: /var/lib/cwl/stg68cf148a-c030-480e-aa27-c02989d31d26/dqc_reference
[2023-06-27 00:33:11,185] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 00:33:11,186] [INFO] Task started: Prodigal
[2023-06-27 00:33:11,186] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3274743-6b8d-472f-8c98-f7f8123b8919/GCA_026391095.1_ASM2639109v1_genomic.fna.gz | prodigal -d GCA_026391095.1_ASM2639109v1_genomic.fna/cds.fna -a GCA_026391095.1_ASM2639109v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 00:33:19,147] [INFO] Task succeeded: Prodigal
[2023-06-27 00:33:19,148] [INFO] Task started: HMMsearch
[2023-06-27 00:33:19,148] [INFO] Running command: hmmsearch --tblout GCA_026391095.1_ASM2639109v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68cf148a-c030-480e-aa27-c02989d31d26/dqc_reference/reference_markers.hmm GCA_026391095.1_ASM2639109v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 00:33:19,411] [INFO] Task succeeded: HMMsearch
[2023-06-27 00:33:19,413] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc3274743-6b8d-472f-8c98-f7f8123b8919/GCA_026391095.1_ASM2639109v1_genomic.fna.gz]
[2023-06-27 00:33:19,442] [INFO] Query marker FASTA was written to GCA_026391095.1_ASM2639109v1_genomic.fna/markers.fasta
[2023-06-27 00:33:19,443] [INFO] Task started: Blastn
[2023-06-27 00:33:19,443] [INFO] Running command: blastn -query GCA_026391095.1_ASM2639109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68cf148a-c030-480e-aa27-c02989d31d26/dqc_reference/reference_markers.fasta -out GCA_026391095.1_ASM2639109v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 00:33:20,067] [INFO] Task succeeded: Blastn
[2023-06-27 00:33:20,073] [INFO] Selected 24 target genomes.
[2023-06-27 00:33:20,073] [INFO] Target genome list was writen to GCA_026391095.1_ASM2639109v1_genomic.fna/target_genomes.txt
[2023-06-27 00:33:20,085] [INFO] Task started: fastANI
[2023-06-27 00:33:20,086] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3274743-6b8d-472f-8c98-f7f8123b8919/GCA_026391095.1_ASM2639109v1_genomic.fna.gz --refList GCA_026391095.1_ASM2639109v1_genomic.fna/target_genomes.txt --output GCA_026391095.1_ASM2639109v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 00:33:36,812] [INFO] Task succeeded: fastANI
[2023-06-27 00:33:36,812] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68cf148a-c030-480e-aa27-c02989d31d26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 00:33:36,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68cf148a-c030-480e-aa27-c02989d31d26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 00:33:36,819] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 00:33:36,819] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 00:33:36,819] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Sediminibacterium ginsengisoli	strain=DSM 22335	GCA_900167075.1	413434	413434	type	True	76.985	50	552	95	below_threshold
Sediminibacterium salmoneum	strain=NBRC 103935	GCA_000511175.1	426421	426421	type	True	76.4218	76	552	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	76.2975	65	552	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 00:33:36,821] [INFO] DFAST Taxonomy check result was written to GCA_026391095.1_ASM2639109v1_genomic.fna/tc_result.tsv
[2023-06-27 00:33:36,822] [INFO] ===== Taxonomy check completed =====
[2023-06-27 00:33:36,822] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 00:33:36,822] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68cf148a-c030-480e-aa27-c02989d31d26/dqc_reference/checkm_data
[2023-06-27 00:33:36,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 00:33:36,853] [INFO] Task started: CheckM
[2023-06-27 00:33:36,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026391095.1_ASM2639109v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026391095.1_ASM2639109v1_genomic.fna/checkm_input GCA_026391095.1_ASM2639109v1_genomic.fna/checkm_result
[2023-06-27 00:34:05,346] [INFO] Task succeeded: CheckM
[2023-06-27 00:34:05,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.19%
Contamintation: 5.21%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-27 00:34:05,377] [INFO] ===== Completeness check finished =====
[2023-06-27 00:34:05,378] [INFO] ===== Start GTDB Search =====
[2023-06-27 00:34:05,378] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026391095.1_ASM2639109v1_genomic.fna/markers.fasta)
[2023-06-27 00:34:05,379] [INFO] Task started: Blastn
[2023-06-27 00:34:05,379] [INFO] Running command: blastn -query GCA_026391095.1_ASM2639109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68cf148a-c030-480e-aa27-c02989d31d26/dqc_reference/reference_markers_gtdb.fasta -out GCA_026391095.1_ASM2639109v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 00:34:06,144] [INFO] Task succeeded: Blastn
[2023-06-27 00:34:06,148] [INFO] Selected 14 target genomes.
[2023-06-27 00:34:06,149] [INFO] Target genome list was writen to GCA_026391095.1_ASM2639109v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 00:34:06,158] [INFO] Task started: fastANI
[2023-06-27 00:34:06,158] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3274743-6b8d-472f-8c98-f7f8123b8919/GCA_026391095.1_ASM2639109v1_genomic.fna.gz --refList GCA_026391095.1_ASM2639109v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026391095.1_ASM2639109v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 00:34:12,288] [INFO] Task succeeded: fastANI
[2023-06-27 00:34:12,307] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 00:34:12,307] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_017987615.1	s__Sediminibacterium sp017987615	86.9881	300	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903958045.1	s__Sediminibacterium sp903958045	86.8496	443	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.78	99.78	0.90	0.90	2	-
GCA_018971025.1	s__Sediminibacterium sp018971025	85.9047	385	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831935.1	s__Sediminibacterium sp903831935	77.2248	131	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.28	98.68	0.92	0.87	6	-
GCA_017856545.1	s__Sediminibacterium sp017856545	77.2105	93	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299885.1	s__Sediminibacterium sp002299885	76.9465	87	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016741945.1	s__Sediminibacterium sp016741945	76.8841	71	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009928005.1	s__Sediminibacterium sp009928005	76.8317	101	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.65	99.49	0.90	0.88	3	-
GCA_009693615.1	s__Sediminibacterium sp009693615	76.799	84	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929425.1	s__Sediminibacterium sp903929425	76.7428	82	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004294465.1	s__Sediminibacterium sp004294465	76.5636	60	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903825095.1	s__Sediminibacterium sp903825095	76.2702	58	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.41	98.41	0.71	0.71	2	-
GCA_013297995.1	s__Sediminibacterium sp013297995	76.0917	75	552	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 00:34:12,309] [INFO] GTDB search result was written to GCA_026391095.1_ASM2639109v1_genomic.fna/result_gtdb.tsv
[2023-06-27 00:34:12,310] [INFO] ===== GTDB Search completed =====
[2023-06-27 00:34:12,313] [INFO] DFAST_QC result json was written to GCA_026391095.1_ASM2639109v1_genomic.fna/dqc_result.json
[2023-06-27 00:34:12,313] [INFO] DFAST_QC completed!
[2023-06-27 00:34:12,313] [INFO] Total running time: 0h1m3s